2.4 Tool-wide comparison
MeStudio provides a novel amount of feature-level information that is not present in other widely used genomic software packages. For instance, Bedtools (https://bedtools.readthedocs.io/en/latest/) is a well-known toolset for genomic applications through which it is possible to detect methylation features regarding CpG island, but it is not possible to extract information about CDS, nCDS, tIG and US regions as it does not provide any figure about methylated motif occurrences. Bioconductor also supplies packages that can be used for methylation analysis such as “GenomicRanges ” (https://bioconductor.org/packages/release/bioc/html/GenomicRanges.html) and “motifmatchr ” (https://bioconductor.org/packages/release/bioc/html/motifmatchr.html). GenomicRanges allows to split the genome in predefined intervals but no information about the genomic feature is produced. The packagemotifmatchr allows to find motifs along the genome but no gene or protein annotations are included in the output. Moreover, MeStudio simply takes as input for the motifs a text file which is a more user-friendly format compared to the one required by motifmatchr . Table 1 provides a comparison of the features of MeStudio and possible alternative tools.